Vojtěch Kulvait
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/blima |
| Branch: RELEASE_3_9 |
| Last Commit: 30cee8f |
| Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:30:05 -0400 (Wed, 16 Oct 2019).
| Package 178/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| blima 1.18.0 Vojtěch Kulvait
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: blima |
| Version: 1.18.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings blima_1.18.0.tar.gz |
| StartedAt: 2019-10-16 02:18:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:21:20 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 157.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: blima.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blima.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings blima_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/blima.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'blima/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'blima' version '1.18.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'blima' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
nonParametricEstimator: no visible global function definition for 'var'
performXieCorrection: no visible global function definition for 'dnorm'
performXieCorrection: no visible global function definition for 'pnorm'
vstFromLumi: no visible global function definition for 'lm'
vstFromLumi: no visible global function definition for 'predict'
Undefined global functions or variables:
dnorm lm pnorm predict var
Consider adding
importFrom("stats", "dnorm", "lm", "pnorm", "predict", "var")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) interpolateSortedVectorRcpp_.Rd:0-21: Must have a \description
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/blima/libs/i386/blima.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/blima/libs/x64/blima.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/blima.Rcheck/00check.log'
for details.
blima.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/blima_1.18.0.tar.gz && rm -rf blima.buildbin-libdir && mkdir blima.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=blima.buildbin-libdir blima_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL blima_1.18.0.zip && rm blima_1.18.0.tar.gz blima_1.18.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 36866 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 36866 100 36866 0 0 171k 0 --:--:-- --:--:-- --:--:-- 177k
install for i386
* installing *source* package 'blima' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c interpolateSortedVector.cpp -o interpolateSortedVector.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o blima.dll tmp.def RcppExports.o interpolateSortedVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/blima.buildbin-libdir/00LOCK-blima/00new/blima/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'blima'
finding HTML links ... done
aggregateAndPreprocess html
bacgroundCorrect html
bacgroundCorrectSingleArray html
backgroundChannelSubtract html
backgroundChannelSubtractSingleArray html
blima-package html
channelExistsIntegrityWithLogicalVectorList
html
checkIntegrity html
checkIntegrityLogical html
checkIntegrityOfListOfBeadLevelDataObjects
html
checkIntegrityOfSingleBeadLevelDataObject
html
chipArrayStatistics html
createSummarizedMatrix html
doAction html
doProbeTTests html
doTTests html
filterBg html
getNextVector html
initMeanDistribution html
insertColumn html
interpolateSortedVector html
interpolateSortedVectorRcpp_ html
log2TransformPositive html
meanDistribution html
nonParametricEstimator html
nonPositiveCorrect html
nonPositiveCorrectSingleArray html
numberOfDistributionElements html
performXieCorrection html
plotBackgroundImageAfterCorrection html
plotBackgroundImageBeforeCorrection html
quantileNormalize html
readToVector html
selectedChannelTransform html
selectedChannelTransformSingleArray html
singleArrayNormalize html
singleChannelExistsIntegrityWithLogicalVector
html
singleCheckIntegrityLogicalVector html
singleNumberOfDistributionElements html
updateMeanDistribution html
varianceBeadStabilise html
varianceBeadStabiliseSingleArray html
vstFromLumi html
writeBackgroundImages html
xieBacgroundCorrect html
xieBacgroundCorrectSingleArray html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'blima' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c interpolateSortedVector.cpp -o interpolateSortedVector.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o blima.dll tmp.def RcppExports.o interpolateSortedVector.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/blima.buildbin-libdir/blima/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'blima' as blima_1.18.0.zip
* DONE (blima)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'blima' successfully unpacked and MD5 sums checked
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blima.Rcheck/examples_i386/blima-Ex.timings
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blima.Rcheck/examples_x64/blima-Ex.timings
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